[gmx-users] Removing Water from Final Simulation

[Dallas Warren]

What group did you select from the list offered when you ran the script?  Did it include all of your molecules, minus water?  Or did you just select something like "Protein"?

You need to run make_ndx and general a group that contains all of the molecules you want.  So you will want to do something like "1 | 2 | 3" when running make_ndx  What those numbers are depends on what is contained within the gro file you feed it.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Parker de Waal
> Sent: Monday, 3 June 2013 11:53 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Removing Water from Final Simulation
> 
> Thanks Warren for your help, those were exactly the functions I was
> looking
> for!
> 
> However I'm still experiencing a bit of trouble because my simulated
> protein contained a heme cofactor and it seems to only let me extract
> one
> object.
> 
> Have you had any experience with this?
> 
> Parker
> On Sun, Jun 2, 2013 at 9:47 PM, Dallas Warren
> <Dallas.Warren at monash.edu>wrote:
> 
> > trjconv for trajectories
> > editconf for coordinate files
> >
> > Along with an appropriately generated index file (using make_ndx)
> which
> > contains the molecules you want in the output within a single group.
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> > Drug Discovery Biology
> > Monash Institute of Pharmaceutical Sciences, Monash University
> > 381 Royal Parade, Parkville VIC 3052
> > dallas.warren at monash.edu
> > +61 3 9903 9304
> > ---------------------------------
> > When the only tool you own is a hammer, every problem begins to
> resemble a
> > nail.
> >
> >
> > > -----Original Message-----
> > > From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> > > bounces at gromacs.org] On Behalf Of Parker de Waal
> > > Sent: Monday, 3 June 2013 11:10 AM
> > > To: gmx-users at gromacs.org
> > > Subject: [gmx-users] Removing Water from Final Simulation
> > >
> > > Hi GMX users!
> > >
> > > I just completed my first 30 ns simulation and would to remove all
> > > water
> > > molecules from the resulting .gro and trajectory files for the sake
> of
> > > my
> > > HDD.
> > >
> > > Does anyone know how to do this?
> > >
> > > Cheers,
> > > Parker
> > > --
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